HALI's now famous Dr. Popo (Zikankuba Sijali, the bat doctor), Chris Kilonzo, and our newly minted One Health Officer, Alphonce Msigwa have been hard at work scoping sites and sampling wildlife as part of HALI's zoonotic disease investigations for our PREDICT and viral sharing between human and animal populations projects. They've been sending us field updates on a pretty regular basis over WhatsApp, which is proving to be a great tool for real-time situational awareness. Plus with that hardcore encryption it even passes HIPAA standards so is certified secure for protecting the privacy of our stakeholders and research participants.

One of the team's latest updates came from Chita, a small village in the Udzungwa Mountains area of Tanzania where our team has been working with a local health clinic to sample patients with febrile illnesses to find out if there are fevers of unknown origin that may be zoonotic and potentially caused by viruses transmitted by wildlife like bats that often roost in people's homes or from monkeys in local forests where people frequently go to hunt, gather, and spend time. Who doesn't love a forest?

I scraped the pics in this slideshow from our WhatsApp feed and added Zika's captions along with a few of my own for clarity to highlight one day in the life of this bat sampling crew, this time working in a village setting targeting micro bats that roost in the roofs of homes and prove to be quite a nuisance for the Chita residents. Thanks to Zika and our One Health Officer's efforts, the HALI team has been doing a good job sticking up for bats and promoting conservation for the ecosystem services they provide (eating insects and mosquitoes a huge one in an endemic malaria zone). But there is certainly a lot of work to be done to mitigate the risks for disease transmission, even some easy fixes like low cost improvements to homes to prevent the bats from moving in and taking up residence by adding screens and repairing ceiling panels. But low cost is not no cost, so until there is a Chita Champion the HALI team will keep working with the community on zoonotic disease outreach and prevention ideas.

WhatsApp feed

A screenshot of our team's WhatsApp feed keeping our international team up to speed on the great work HALI does in the field.

Welcome to Chita

Welcome to Chita. Population.... ?

Where are the bats?

Wandering the streets looking for signs of bats.

Our trusted guide

Children are often the best local guides. With plenty of time to play and explore and their natural curiosity, they are great for helping find wildlife like bats.

Bat roosts

Finding local bat roosts in the eaves and under roofs of local homes

Roof damage

Ceilings like these are great for bats to get up into the roof where they can live uninterrupted and really bother the people below with guano and urine, then smell and noise.

In East Africa, HALI is helping partners from Addis Ababa University, the implementing partner for the PREDICT project in Ethiopia, learn safe capture and sampling of bats as part of a growing network of African scientists working to improve detection and prevention of emerging pandemic threats. The slideshow below gives a great look at the training:

Bats at the Nunge site roost on large trees surrounded by homes and offices seen in the background.

A trapped straw colored fruit bat (Eidolon helvum).

The team about to sample a bat.

The PREDICT Ethiopia team met Zikankuba Sijalia, HALI's PREDICT project coordinator, at a recent global meeting and plans were made to bring the Ethiopian team to Tanzania to learn from Dr. Popo himself (the bat doctor, Zika's superhero name), who is quickly becoming one of the premier bat experts in the East Africa region.

HALI's project scientist Chris Kilonzo took some amazing photos of the first day of training, conducted in Morogoro, Tanzania at a fruit bat roosting site in trees near the campus of Sokoine University, one of the sites the team is surveying as part of HALI's Viral Sharing project.

The team will continue to work with their new Ethiopian friends on bat and non-human primate sampling in the Udzungwa Mountains over the next few weeks. According to the HALI team, the Ethiopian scientists are a quick study and after only a few days in Tanzania are already mastering the skills and techniques for bat surveillance. Back home in Ethiopia, the Addis Ababa team will use these newly acquired skills in surveillance activities targeting bats as potential hosts for MERS Coronavirus and other potentially zoonotic viruses.

Look out for more news on Dr. Popo and the HALI team soon as field activities ramp up!

-David
Wolking

“For a time, all
was bountiful in the land, but then drought came. No rain fell for months, and
it became drier and drier, hotter and hotter. The stream stopped flowing. The
water hole turned first to mud and then to dry, cracked earth. One by one, the animals slowly left or
starved until no one was left…” - Lion, Chameleon
and Chicken, A Gogo Bantu Folktale from Tanzania

Ruaha River drying

The Great Ruaha River, once flowing year round, experiences reduced flow in the East African dry season - a factor brining wildlife populations into close proximity and increasing potential disease transmission.

Baboons

Baboons rest in the shade in the Ruaha Ecosystem. The HALI team detected Mycobacterium bovis, which can cause tuberculosis, in yellow baboons and other wildlife in Ruaha, and is exploring the transmission dynamics of M. bovis among wildlife, livestock, and human communities in the area. (Photo by L. Vanwormer).

Boy helps with sampling

A young Maasai boy assists the HALI team while they sample livestock for tuberculosis. HALI has detected Mycobacterium bovis in livestock, which causes bovine tuberculosis - a zoonotic disease. Through NIH funding, HALI is working with pastoralists, villagers, and the National Institute of Medical Research to sample the environment, domestic and wild animals, and people for tuberculosis. This research will help HALI design ecosystem-based management strategies for tuberculosis prevention and control. (Photo by D. Clifford)

Dr. Alex trains the team

Dr. Alex, a HALI team member and veterinarian for Ruaha National Park, trains park and community game scouts in recognizing signs of disease in dead wild animals. HALI recruited rangers and scouts and established a novel wild animal carcass surveillance program in Ruaha to sample dead animals (hunted, killed, poached, or from natural causes) for disease causing pathogens. (Photo by D. Clifford).

Coaster

Coaster, one of HALI's lead game scouts on the wild animal carcass surveillance program reports his latest discoveries to HALI researchers. (Photo by D. Clifford).

HALI game scouts

Scouts working with HALI investigate an impala carcass. On a typical day, the scouts would receive a report from community members about a dead animal, sometimes a baboon shot while raiding crops, or dik dik or impala killed for meat. The scouts then ride out to the scene and collect samples for HALI, storing them in a solar-powered freezer at the HALI field station in Tungamalenga village. (Photo by D. Clifford).

Shukuru

Shukuru, HALI's lead game scout places samples in a cooler for preservation until HALI veterinarians can process the samples for laboratory work at the HALI lab at Sokoine University of Agriculture. (Photo by D. Clifford)

Deana

Dr. Deana Clifford, the study's lead author and program coordinator, worked with a team of experts at Sokoine University of Agriculture to process the animal samples and test them for Mycobacterium bovis, which can cause tuberculosis in animals and people. (Photo by J. Erickson)

Khadijah

Khadijah, one of HALI's laboratory technicians works on samples under a biosafety cabinet, to ensure the lab team is well protected from any disease causing agents as they work to detect mycobacterium in the HALI samples. (Photo by D. Porter).

Buffalo

The HALI wild animal carcass surveillance program led by Deana Clifford detected Mycobacterium bovis in multiple wildlife species in the Ruaha Ecosystem. This study is the first to confirm M. bovis infection in African Buffalo herds in Tanzania. (Photo by W. Miller)

Meat market

Livestock markets like this one in the Iringa District of Tanzania roast meat from cattle and other animals, a favorite dish for many in the area from pastoralists to members of the HALI team. The roasting, when done thoroughly, can kill off the bacteria, but the real risk for disease transmission may be when the meat is butchered and processed. HALI is working with the community in the Ruaha area to better understand routes of tuberculosis transmission to design appropriate prevention and control measures for animals and people. (Photo by D. Wolking)

Change is coming. It was first recognized in the landscape, when the Great
Ruaha River in Tanzania, the lifeblood of a land where miombo woodlands of
Southern Africa blend into the Sudanian Acacia-Commiphora
zone of East Africa, slowly
dried up.
That seasonal drying, along with other changes in the landscape,
agricultural intensification, deforestation, extension of grazing lands into
protected areas, may be the source of other less noticeable changes,
microscopic changes.

In the Ruaha ecosystem, home to Tanzania’s
largest national park and protected area, researchers with the Health for
Animals and Livelihood Improvement (HALI)
project are investigating how these changes at both
the landscape and microscopic level affect the health of wildlife, domestic animal
and human communities. In a new
publication released in June, HALI researchers report
the detection of Mycobacterium bovis, a
bacterium that can cause tuberculosis in animals and humans, in 8 species of
wildlife, including the first detection of M.
bovis, in 3 new species: Kirk’s Dik Dik, vervet
monkeys, and yellow baboons. In addition, the
team detected M. bovis in African
buffalo inside Ruaha National Park, the first confirmed buffalo infection in
Tanzania.

“Although
we anticipated we might find bovine tuberculosis in species closely related to
cattle, like buffalo, the documentation of infection in 8 different species
occupying different ecological niches both within and outside wildlife
protected areas was unexpected and suggests the existence of a complex
wildlife-livestock transmission cycle.” - Dr. Deana Clifford, founding HALI project coordinator and wildlife
veterinarian for the California Department of Fish and Wildlife

The microbial market place

In Ruaha, M.
bovis is not a stranger, at least to domestic animals and their caretakers. There is wide spread bovine
tuberculosis (bTB) in cattle in the area, and as a zoonotic pathogen,
tuberculosis may also affect human communities. The HALI team looked at bTB in livestock, and observing the
land-use changes in the Ruaha area, hypothesized that tuberculosis was also infecting
wildlife populations. Livestock herds frequently share grazing lands, foraging
areas, and water holes with wildlife, and as a result may swap microbes and
parasites with other species through environmental contamination, or in the
case of M. bovis, even through
aerosols, through a cough or a sneeze.

From 2006-2010, HALI worked with game scouts
employed by the Community Wildlife Management Areas bordering Ruaha National
Park, hunting companies, Park staff, and village networks to obtain tissue
samples from hunter-killed, depredated animals (animals killed for causing crop
damage in fields), and carcasses.
Two HALI game scouts, Coaster and Shukuru, social network nodes for news of animal deaths, would hear about
a kill or a carcass and bicycle out into the bush to collect tissue samples and
GPS the location. Samples were
then sent to the project laboratory at the Sokoine University of Agriculture, a
center of excellence for molecular diagnostics and tuberculosis detection.

The team collected tissues from 149 animals
of 30 different species, the majority (69%) collected outside protected areas
in village lands. Sokoine
University cultured the samples for mycobacterium
and used PCR assays to detect M. bovis. Positive samples were spoligotyped (a
technique used to delineate mycobacterium
species and distinguish unique strains), and they found that M. bovis isolates from infected wildlife
were identical to the strains of M. bovis
found in livestock herds. In an
area where human settlements, activities and livestock grazing areas are
pushing further and further into wildlife habitat, the animals are
trading. They just don’t know it, and
it is possible that this microbial trade could be making them sick.

Although the team’s findings suggest that
livestock herds and wildlife are sharing M.
bovis, it is not clear who started it. With M. bovis-infected
African buffalo herd inside Ruaha National Park, a herd that encounters
livestock rarely, and little to no bovine tuberculosis control among livestock
in the area, it is possible M. bovis
is maintained in the ecosystem by both wildlife and livestock. Because the team found M. bovis in wildlife species occupying
very different ecological niches, from buffalo to other ungulates like dik diks
and impala all the way up the evolutionary chain to our primate cousins vervet
monkey and yellow baboon, it appears that M.
bovis is settled down and is planning to stay. Buffalo in particular are a major maintenance host for
bovine tuberculosis in Africa, once bTB is established in a free-ranging herd,
that herd can sustain infection without repeated trade of M. bovis with other animals like livestock. In other words, M. bovis becomes a resident, and since buffalo are often preyed on
or scavenged by carnivores and other wildlife, the microbe can spillover to
other species in the ecosystem, even humans like hunters. In Tanzania wild meat is usually smoked
or roasted, nyama choma, but before you have meat you must have a butcher, and field
dressing a carcass without appropriate hygiene and sanitation measures can be a risk for exposure to bTB.

Regulating the exchange?

Now that M.
bovis seems to be a microbial resident in both livestock and wildlife in
the area, how do you control its spread?
The HALI team identify several management options in the article, but
for a pathogen intrinsically linked to multiple species in different ecological
niches, these management options require an ecosystem-based approach linking
livestock and human health interventions with conservation and development goals.

The Ruaha River is drying, and if that
continues, the health of the entire ecosystem will suffer. The good news is that continuing and
enhancing current conservation efforts to improve hydrologic flow, prevent bank
erosion and improve water quality will increase water abundance, allowing more
spaces for animals to drink and limiting interspecies contact.

Ecological restoration and
conservation efforts should be expanded to preserve remaining wildlife habitat
and help address wildlife forays into village land, farms, and grazing
areas.

The veterinary community can target
test of cattle and wildlife for bTB and a range of other diseases in shared
grazing lands to identify areas or sites with increased spillover risk, and
work to better understand livestock grazing strategies, locations, and sites to
improve planning for pasture access and livestock production.

Finally, and perhaps most critical is
improving livelihoods. Increasing
income to rural residents through poverty reduction programs, increased market
access, training and education can reduce reliance on natural resources for
survival, the driving force behind land use change that may be undermining
ecological health and driving M.bovis
and other zoonotic disease transmission dynamics.

In this approach, conservation is linked to development – with more water from a flowing river, better grazing opportunities, healthier livestock, and improved livelihoods, the pressure for livestock and wildlife to share resources, interact, and exchange microbes can be reduced, and the animals, along with their caretakers, will not have to slowly leave the water holes until no one is left.

The HALI team works with Ruaha National Park veterinarians to safely restrain an adult giraffe for sampling. Giraffes in the park have been suffering from a skin disease, leading to a partnership between the park, HALI, and Sokoine University to identify the cause of the disease and intervention options. (Photo by Goodluck Paul)

HALI Partnerships with the Tanzania Wildlife Research Institute and National Parks

- Goodluck Paul and
David Wolking

In May 2013, HALI project veterinarians,
including project leads Dr. Jonna Mazet and Professor Rudovick Kazwala, were
invited by RUNAPA to participate in a giraffe immobilization exercise to collect
samples for an investigation into an emerging skin disease impacting giraffe herd health at the park. In collaboration
with RUNAPA veterinarians, Serengeti National Park veterinarians and other
staff from the Sokoine University of Agriculture (SUA), the team safely immobilized
16 giraffes, and samples were sent to SUA for laboratory investigation. Once the samples are analyzed, results
will be shared with the park staff, and options for skin disease intervention will be carefully considered.

We were able to document the immobilization event in our slide show (see Twiga Take-Down). It is no small feat to safely inject
drugs and guide Earth’s tallest terrestrial animal to ground-level for
sampling, and even more difficult to get them back on their feet again, but the team did an excellent job ensuring no giraffes were injured,
and that all animals safely recovered and returned to their lives browsing on twigs and
leaves from tops of acacia trees, ruminating on life, necking, and tending to
young calves.

What’s on the table now?

This month in northern Tanzania, HALI’s PREDICT project is
training TAWIRI wildlife veterinarians in the safe capture, handling and
sampling of small mammals like bats in the Tanga and Arusha regions.
PREDICT is investigating bats as a potential animal host species for
zoonotic diseases, and is sampling bat colonies and roosting sites throughout
Tanzania.

Later this year, in mid or late September, HALI is planning another
collaborative activity with Ruaha
National Park and TAWIRI to conduct an aerial and ground survey of
buffalo populations in the southern part of the Park. These surveys help the park better understand the buffalo population and herd health, and assist in park wildlife management plans.

Future collaborations?

HALI looks forward
to fostering other collaborations and sharing project experience on disease
surveillance, animal handling, and investigations into emerging and re-emerging
infectious diseases throughout the country. We hope these partnerships are just the beginning, and that
we continue to join forces with the National Parks, TAWIRI and others to better
understand disease and improve health at the wildlife-human-livestock and
environmental interfaces in Tanzania.

- David Wolking

The caves were interesting, full of bats. At this chamber you could just hear all the bats surrounding you and when the guide point to the inside of the chamber you could see hundreds of bats just flying around. - Melvin (a tourist in Tanzania at the Amboni Caves, Tanga Region)

Cave tourism sounds like a great time. You shimmy down through a limestone tunnel into a large cavern in the dark, headlamps shining sporadically on stalactites and casting eery shadows, the echo of your voice and of dripping water, and the chirping of cave bats. Cave tourism also means big business. Mammoth Cave National Park generates an estimated $64 million for the south central Kentucky area each year.

But cave tourism also presents certain risks. Beyond the fear of headlamps dying out leaving you in the dark bowels of the earth without Batman's utility belt and his famous nightvision Bat-goggles, there is the risk of disease both to you and to those happily chirping and roosting bats.

If you somehow missed the plethora of news reports, White-nose Syndrome (WNS), a fungus infecting bats and causing them to awake more often during hibernation, has been associated with the deaths of 5-6 million North American bats. The rapid spread of WNS and uncertainty about its spread and transmission has lead the US Fish and Wildlife Service to declare a moratorium on caving activities in affected regions, as it is suspected that the fungus is transported through soil via clothing and boots of cavers.

But bats are not the only ones that can get sick when hanging out with people in caves. We know bats harbor a lot of disease causing organisms, including viruses like rabies, Marburg, and coronaviruses like SARS, and people visiting caves have been infected and in some cases even died from these viruses.

Caves are fascinating ecosystems, and cave-dwelling bats live in amazingly social, interesting colonies. A recent article in PLOS Pathogens describes the behavioral characteristics of Egytian fruit bats in Python Cave, Uganda, a popular cave tourist destination associated with recent Marburg virus outbreaks. In Python, the fruit bats compete for roosting space in the cave, with juvenile sub-adult bats dwelling in less secure locations in tight clusters near the floors and cave entrance, locations with higher risk of predation (it is after all Python Cave), and where they get shit on. Literally. Roosting near the floor of the cave means all your relatives and elders above urinate and defecate on your head, a risk factor for viral exposure the researchers speculate is linked to seasonal pulses of Marburg virus circulation in this sub-adult demographic. So, to make a long story short, all that guano cave tourists are trudging through could be infectious, it could make you sick.

I stress that it could make you sick because in a lot of cases we don't really know. Even in the Python Cave study, the researchers were unable to detect Marburg virus in the bat guano. But we do know people visiting caves, or working in mines or abandoned mine shafts have gotten sick from viruses linked to bats in the past, and have died. The risk is there. Cave tourists beware.

What does this have to do with HALI?

"We went caving at the Amboni caves (home to more bats than I would have liked!)" - Christine

Our PREDICT project field team is in northern Tanzania this month capturing bats and rodents at high-risk human-wildlife contact interfaces, like the cave tourism context, where people might get sick from wild animals. One of the places they are visiting is the Amboni Caves, where our friend Melvin (quoted above) saw so many bats. Amboni is a popular tourist destination and the largest cave system in East Africa. Lonely Planet even advises cave visitors to "wear closed toed shoes to avoid picking bat droppings off your feet." Nice - some inadvertent disease risk prevention advice from the travel gurus!

We hope to capture and sample some of the Amboni cave bats and investigate them for viruses that may be harmful to people. By looking at bat feces (and other samples), we can determine if there are infectious disease risks to cave visitors and other high-risk groups like the cave guides. If Zika brought his utility belt, we may even get some good pictures from Amboni to share, so tune in soon, "same bat-time, same bat-channel..."

Rodents are a popular delicacy in Southern Tanzania and Malawi. Photo from "Eating Roasted Mice in Malawi" via The Daily Mail.

- David Wolking

In certain areas along the Indian Ocean coast from Kenya to Malawi (and likely beyond), mice hunting, rat trapping, and rodent roasting can be pretty popular. Rodents are actually a common source of protein worldwide, even in Paris, where rats were eaten on a large scale during the Franco-Prussian War and reportedly taste like partridge and pork. There is even a recipe in Larouse Gastronomique for Entrecote à la bordelaise (Bordeaux style grilled rat), and it looks delicious.

Over the weekend, Zika and the field team returned from the Mtwara region in Southern Tanzania, where they worked with the Ward Councilor and village leaders to learn about rodent hunting and consumption, and partnered with local hunters to trap the popular delicacies for sampling. We know rodents, especially mice like Mastomys natalensis (the Natal multimammate mouse) are reservoir hosts for zoonotic viruses like Lassa Fever in Sub-Saharan Africa, and the hunting and consumption of wild meat is a risky practice for disease emergence. When we learned about the popularity of roasting mice in the area, sampling in Mtwara became a priority for disease surveillance as part of the USAID-funded PREDICT project.

After introducing PREDICT to the local leaders and identifying some hunters to help guide them towards prime trapping zones, the team captured 50 rodents (mainly field mice) in 3 different villages. As part of our disease outreach program, the team also talked with the hunters and local leaders about the risks of zoonotic diseases, and ways to minimize disease transmission between people and rodents. It seems rodent hunting is a popular activity for both children and adults in the area, and larger rodents fattened on grain after a harvest can sometimes feed several people. Hunters capture the rodents in locally made traps, and are typically roasted (nyama choma - barbecued meat). Cooking meat well is a good practice to destroy viral RNA that might cause diseases like Lassa Fever, and the HALI team did their best to communicate other risks involved in disease transmission from rodents like bites during trapping, cuts during butchering, or even inhaling aerosolized urine or feces if the animals were in the local traps for a time before removal for the big barbecue.

With the samples packed up in liquid nitrogen, the team transported them back to Sokoine University of Agriculture in Morogoro. There, Ruth Maganga, PREDICT's laboratory technologist will process them and extract the RNA, and prepare them for viral screening to determine if any of the rodents we sampled were shedding viruses, and ultimately if those viruses might pose a threat to human health.

The PREDICT team at Tandale market chatting up the market manager about Ratatouille in November.

- David Wolking

Today the PREDICT team led by Zika and Goodluck laid their first traps at the Tandale market in Dar es Salaam. This kicks off a new phase for PREDICT, where we begin trapping at high-risk urban areas for human and wildlife contact. For us in the US, "urban" contact with wildlife usually means throwing whatever is handy at mice, rats, or raccoons, or maybe feeding ducks and pigeons. In Dar, it's really not that different, except they have fruit bats, and it's nothing like the US at all, I lied. The first site Zika chose for sampling is one of the biggest markets in town, full of delicious looking fruits and vegetables, and according to the Tandale market manager, full of rodents.

After talking with the market manager and getting the market guards to guarantee the safety of our traps overnight, Zika and Goodluck set out a trapping grid in the early evening, and will head on back to the market at 3:30AM to check the traps, and if we're lucky, do some very minimal and safe sampling.

I'm expecting these market mice to be foodies, Tandale is a magical place for the culinarily inclined. I'm sure if Remy lived in Dar, he'd live in Tandale and whip up a magical curry rich in Zanzibari spices, coconut milk, and pili pili... Maybe Pixar will do a Ratatouille 2: Swahili Coast edition. Pixar? Pixar are you there? It's me Remy and I want to go to Tanzania!

- David Wolking

"The role of disease in wildlife populations has probably been radically underestimated" - Aldo Leopold

So begins the special issue Disease Package in the Wildlife Professional, the quarterly magazine of the Wildlife Society. In case you missed this last Spring, you need to check it out. Why? Because it's amazing and everyone loves packages. Even disease packages. As a special treat for HALI fans, our very own Drs. Deana Clifford and Jonna Mazet have a special feature on page 20 "One Health Drives Wildlife Vets". There are also great contributions on why disease is relevant in wildlife conservation, the role of disease in marine ecosystems, and of course on infectious disease spillover, that often referenced human-animal interface we spend so much of our time investigating through projects like HALI and PREDICT. So check it out, and if you like it, consider supporting the Wildlife Society so they can keep making these great publications and give us more packages!

- David Wolking

If you're a person who's wandered through the forest and come across a dead animal or a carcass, or been driving down a country road and spotted road kill and wondered "Hey, maybe that thing was killed by some crazy infectious disease!" then you're in the right place. Once you enter the world of disease it's really hard to look at life (or death) the same way again.

Check it out and let us know what you think, this handbook is supposed to be interactive - we even developed some excellent case studies to put you right in the thick of some crazy situations (rabid dogs and hyenas anyone?). For our East African friends, we even have a version in Kiswahli. Soma! Thanks to the US Fish and Wildlife Service Wildlife Without Borders project for supporting this initiative, along with the Tanzania National Parks and MBOMIPA community game scouts who actually do stumble upon dead wildlife and need to know this stuff.

HALI Project

The Health for Animals and Livelihood Improvement (HALI) project works with local stakeholders to investigate health at the human-animal-environment interface in Tanzania.

Join the HALI Team...

HALI is supported by grant funding, awards, and through the contributions of our network of dedicated volunteers and team members. To ensure sustainability of our programs and to keep our talented teams and activities funded, HALI relies upon philanthropic support from private donors. Please consider supporting the HALI project by visiting our donation center at the UC Davis Wildlife Health Center.